Keywords are paired combinations of a category and a value that pertain to the cytometric data contained in a workspace.

Keyword values can either be imparted to the FCS data file at the time of collection, or added post-acquisition in FlowJo.  In either case they are accessible through FlowJo, and are useful for organizing data.  FCS is an acronym for Flow Cytometry Standard.  It is essentially the set of rules that cytometer manufacturers follow when creating their data output format, and it includes a required set of keywords that must be written to the header portion of an FCS file.

This page contains a list of the special keywords defined as part of the FCS 3.1 Standard, along with a brief description of the corresponding keyword value, as many of the categories do not have particularly descriptive names.  The description of the FCS format on the International Society for the Advancement of Cytometry’s (ISAC) webpage, and the actual standard in PDF form are available at, respectively:

Cytometer manufacturers can add additional proprietary keywords to the files that come from their machines in addition to the required keywords.  These can be distinguished in that the required keywords all start with a $.  Additional keywords can be created from within FlowJo and saved with your workspace (though they will not save with your FCS file(s) as we do not modify your raw data, ever). Click here for more information on adding keywords to the workspace.

Keywords can be used in a Value Series. For information about how FlowJo handles FCS files, go here.

Scientists can use their own keyword identifiers, but they may not start with $, unless it is defined in the specification document.

 

Required Keywords

$BEGINANALYSIS Byte-offset to the beginning of the ANALYSIS segment.
$BEGINDATA Byte-offset to the beginning of the DATA segment.
$BEGINSTEXT Byte-offset to the beginning of a supplemental TEXT segment.
$BYTEORD Byte order for data acquisition computer.
$DATATYPE Type of data in DATA segment (ASCII, integer, floating point).
$ENDANALYSIS Byte-offset to the end of the ANALYSIS segment.
$ENDDATA Byte-offset to the end of the DATA segment.
$ENDSTEXT Byte-offset to the end of a supplemental TEXT segment.
$MODE Data mode (list mode, histogram).
$NEXTDATA Byte offset to next data set in the file.
$PAR Number of parameters in an event.
$PnB Number of bits reserved for parameter number n.
$PnE Amplification type for parameter n.
$PnR Range for parameter number n.
$TOT Total number of events in the data set.
 

Optional Keywords

$ABRT Events lost due to data acquisition electronic coincidence.
$BTIM Clock time at beginning of data acquisition.
$CELLS Description of objects measured.
$COM Comment.
$COMP Fluorescence compensation matrix.
$CSMODE Cell subset mode, number of subsets to which an object may belong.
$CSVBITS Number of bits used to encode a cell subset identifier.
$CSVnFLAG The bit set as a flag for subset n.
$CYT Type of flow cytometer.
$CYTSN Flow cytometer serial number.
$DATE Date of data set acquisition.
$ETIM Clock time at end of data acquisition.
$EXP Name of investigator initiating the experiment.
$FIL Name of the data file containing the data set.
$GATE Number of gating parameters.
$GATING Specifies region combinations used for gating.
$GnE Amplification type for gating parameter number n.
$GnF Optical filter used for gating parameter number n.
$GnN Name of gating parameter number n.
$GnP Percent of emitted light collected by gating parameter n.
$GnR Range of gating parameter n.
$GnN Name used for gating parameter n.
$GnT Detector type for gating parameter n.
$GnV Detector voltage for gating parameter n.
$INST Institution at which data acquired.
$LOST Number of events lost due to computer busy.
$OP Name of flow cytometry operator.
$Pkn Peak channel number of univariate histogram for parameter n.
$PKNn Count in peak channel of univariate histogram for parameter n.
$PnF Name of optical filter for parameter n.
$PnG Amplifier gain used for acquisition of parameter n.
$PnL Excitation wavelength for parameter n.
$PnN Short name for parameter n.
$PnO Excitation power for parameter n.
$PnP Percent of emitted light collected by parameter n.
$PnS Name used for parameter n.
$PnT Detector type for parameter n.
$PnV Detector voltage for parameter n.
$PROJ Name of the experiment project.
$RnI Gating region for parameter number n.
$RnW Window settings for gating region n.
$SMNO Specimen (tube or well) label.
$SRC Source of the specimen (patient name, cell types).
$SYS Type of computer and its operating system.
$TIMESTEP Time step for time parameter.
$TR Trigger parameter and its threshold.
$UNICODE UNICODE code page for string type keyword values.